Coordinated microRNA-mRNA regulatory remodelling across the compressed maturation of the African killifish (Nothobranchius furzeri)

The turquoise killifish (Nothobranchius furzeri) serves as a promising model for studying development and aging due to its rapid maturation and brief lifespan. Researchers explored how microRNA (miRNA) regulation synchronizes gene expression throughout the fish's short developmental stages. By analyzing miRNA and mRNA expression from the same unexposed animals at three distinct points - newly hatched fry (4 weeks), juveniles (~8 weeks), and aged adults (~8 months) - they discovered that miRNA and mRNA profiles followed a consistent pattern from fry to juveniles and adults.

This developmental progression was primarily driven by tissue maturation, as evidenced by the upregulation of crystallin genes linked to lens development. Additionally, over 2,000 genes exhibited differential expression during the transition to the juvenile stage. Genome-wide analysis of 398 developmentally dynamic miRNAs revealed specific miRNAs whose changes in expression were significantly associated with opposing changes in their predicted target genes.

This included conserved developmental regulators from miR-200/141, miR-29, let-7, and miR-34 families, which showed increased expression as their target cohorts diminished during adulthood. Stage-controlled studies further pinpointed miR-34a, miR-29a, miR-29b, miR-15a, and a novel candidate that maintained consistent target relationships regardless of the overall developmental trajectory.

Among these, miR-29 exhibited a particularly robust upregulation during maturation, aligning with its well-established roles in extracellular matrix remodeling, differentiation, and vertebrate aging. In summary, this study unveils coordinated remodeling of essential miRNA-mRNA regulatory programs across the rapid maturation of N. furzeri, providing a foundation for investigating post-transcriptional regulation during vertebrate development in a species with limited miRNA annotation.